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Question: SNP Profiling Tool
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gravatar for sudhantt
23 months ago by
sudhantt • 0
sudhantt • 0 wrote:

Is there any software which explores which gene has high number of SNP/INDELs ? That means for arranging the genes based on No. of SNPs present....
snp • 656 views
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modified 23 months ago by Jennifer Hillman Jackson ♦ 25k • written 23 months ago by sudhantt • 0
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gravatar for Jennifer Hillman Jackson
23 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Yes, there are several choices.

  • One is to perform variant calling on your own data (many are wrapped for Galaxy), then summarize/count by gene or transcript
  • Another is to use public SNP data resources and do the same

These tutorials include variant calling and other operations https://github.com/nekrut/galaxy/wiki. The Galaxy 101 (both parts) is a good place to start as it covers many relevant data manipulations.

Take care, Jen, Galaxy team
ADD COMMENT • link written 23 months ago by Jennifer Hillman Jackson ♦ 25k

Yeah...!! Thanks for your valuable reply. I understood what you have explained. But we can't count for all the genes having SNP. I need the no. of SNPs per particular gene. Help me in this regard if there is any possibilities.

ADD REPLY • link written 23 months ago by sudhantt • 0

Did you review the 101? It covers counting up the number of SNPs overlapping the input BED file given, per exon. If gene names are associated with the exons, a count can be generated per gene (or any linked attribute/data field).

Related question that uses another method/tool: https://biostar.usegalaxy.org/p/16813/

ADD REPLY • link modified 23 months ago • written 23 months ago by Jennifer Hillman Jackson ♦ 25k

Hello, Than you so much. I got Some Idea.

ADD REPLY • link written 23 months ago by sudhantt • 0

Hi, I have another doubt. I did variant analysis. In the order Given Below, ------ Fastq groomer FastQC, Filter FastQ, Bowtie2 Filter SAM/BAM, NGS:Picard (Mark Duplicates), RmDup, MPileup, Varscan, ANNOVAR Annotate VCF---------

I have to choose SNP data-set from my own analysis. So which one i have to give as input. That procedure (Galaxy 101) need bed file. How do i convert. How to convert bam/vcf to bed file. Thank you in advance.

ADD REPLY • link modified 23 months ago • written 23 months ago by sudhantt • 0
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